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Zinc in PDB 4hma: Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain

Enzymatic activity of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain

All present enzymatic activity of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain, PDB code: 4hma was solved by E.A.Stura, C.Antoni, L.Vera, E.Nuti, L.Carafa, E.Cassar-Lajeunesse, V.Dive, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.72 / 1.94
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.870, 98.240, 47.440, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 28.3

Other elements in 4hma:

The structure of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain (pdb code 4hma). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain, PDB code: 4hma:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4hma

Go back to Zinc Binding Sites List in 4hma
Zinc binding site 1 out of 4 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:22.3
occ:1.00
 O22 A:0ZD306 1.9 29.1 1.0
NE2 A:HIS236 2.0 22.8 1.0
NE2 A:HIS230 2.0 17.5 1.0
NE2 A:HIS226 2.1 20.2 1.0
C21 A:0ZD306 2.7 28.8 1.0
O23 A:0ZD306 2.8 26.8 1.0
CD2 A:HIS230 2.8 9.2 1.0
CE1 A:HIS236 2.8 25.6 1.0
CD2 A:HIS226 3.0 17.9 1.0
CD2 A:HIS236 3.0 26.5 1.0
CE1 A:HIS230 3.1 21.0 1.0
CE1 A:HIS226 3.1 19.4 1.0
ND1 A:HIS236 4.0 23.6 1.0
CG A:HIS230 4.1 18.9 1.0
CG A:HIS236 4.1 26.8 1.0
ND1 A:HIS230 4.1 16.6 1.0
C17 A:0ZD306 4.2 27.5 1.0
CG A:HIS226 4.2 19.3 1.0
ND1 A:HIS226 4.2 19.1 1.0
C9 A:0ZD306 4.6 19.6 1.0
C8 A:0ZD306 4.6 24.6 1.0
N16 A:0ZD306 4.7 28.5 1.0
CE A:MET244 4.7 18.3 1.0
NE2 A:GLN227 4.7 27.8 1.0
C10 A:0ZD306 4.8 25.6 1.0
C7 A:0ZD306 4.8 25.5 1.0
C19 A:0ZD306 4.8 23.2 1.0
C25 A:0ZD306 4.9 31.9 1.0
CA A:PRO246 4.9 24.7 1.0
C11 A:0ZD306 5.0 24.4 1.0

Zinc binding site 2 out of 4 in 4hma

Go back to Zinc Binding Sites List in 4hma
Zinc binding site 2 out of 4 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:32.6
occ:1.00
 OD2 A:ASP177 1.9 40.5 1.0
NE2 A:HIS175 2.0 43.3 1.0
ND1 A:HIS203 2.1 28.6 1.0
NE2 A:HIS190 2.2 37.6 1.0
CG A:ASP177 2.7 44.8 1.0
CD2 A:HIS175 2.7 47.6 1.0
OD1 A:ASP177 2.9 42.3 1.0
CE1 A:HIS203 3.0 31.4 1.0
CE1 A:HIS190 3.1 38.5 1.0
CG A:HIS203 3.1 26.8 1.0
CE1 A:HIS175 3.2 45.7 1.0
CD2 A:HIS190 3.3 34.6 1.0
CB A:HIS203 3.5 25.4 1.0
CG A:HIS175 4.0 48.0 1.0
CB A:ASP177 4.1 47.4 1.0
NE2 A:HIS203 4.1 32.7 1.0
ND1 A:HIS175 4.2 46.7 1.0
O A:TYR179 4.2 47.3 1.0
CD2 A:HIS203 4.2 30.3 1.0
ND1 A:HIS190 4.2 34.3 1.0
CE2 A:PHE192 4.3 40.8 1.0
CG A:HIS190 4.3 29.6 1.0
CZ A:PHE192 4.4 36.8 1.0
CZ A:PHE181 4.7 38.1 1.0
CE2 A:PHE181 4.7 35.4 1.0
CB A:TYR179 4.8 48.1 1.0
CA A:HIS203 5.0 26.3 1.0

Zinc binding site 3 out of 4 in 4hma

Go back to Zinc Binding Sites List in 4hma
Zinc binding site 3 out of 4 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:21.9
occ:1.00
 NE2 B:HIS226 2.0 21.9 1.0
O62 A:0ZD306 2.0 19.8 1.0
NE2 B:HIS230 2.1 15.8 1.0
NE2 B:HIS236 2.1 27.8 1.0
C60 A:0ZD306 2.7 22.2 1.0
O61 A:0ZD306 2.9 26.5 1.0
CD2 B:HIS226 2.9 18.2 1.0
CD2 B:HIS230 2.9 14.3 1.0
CE1 B:HIS226 3.0 19.8 1.0
CD2 B:HIS236 3.1 25.9 1.0
CE1 B:HIS236 3.1 29.0 1.0
CE1 B:HIS230 3.1 22.6 1.0
CG B:HIS226 4.1 19.3 1.0
ND1 B:HIS226 4.1 21.5 1.0
CG B:HIS230 4.1 17.2 1.0
C56 A:0ZD306 4.1 21.3 1.0
ND1 B:HIS230 4.2 21.0 1.0
ND1 B:HIS236 4.2 23.4 1.0
CG B:HIS236 4.2 24.8 1.0
C39 A:0ZD306 4.4 23.2 1.0
N40 A:0ZD306 4.6 23.8 1.0
C5A A:0ZD306 4.6 22.4 1.0
C49 A:0ZD306 4.6 22.8 1.0
C59 A:0ZD306 4.7 25.1 1.0
NE2 B:GLN227 4.7 28.6 1.0
CE B:MET244 4.8 21.4 1.0
O A:HOH437 4.8 32.8 1.0
CB B:PRO246 4.8 22.9 1.0
C45 A:0ZD306 4.9 24.1 1.0
C57 A:0ZD306 4.9 25.6 1.0
C48 A:0ZD306 5.0 26.9 1.0
CA B:PRO246 5.0 23.4 1.0

Zinc binding site 4 out of 4 in 4hma

Go back to Zinc Binding Sites List in 4hma
Zinc binding site 4 out of 4 in the Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of An Mmp Twin Carboxylate Based Inhibitor LC20 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:31.6
occ:1.00
 OD1 B:ASP177 2.0 46.0 1.0
ND1 B:HIS203 2.0 24.6 1.0
NE2 B:HIS175 2.0 36.4 1.0
NE2 B:HIS190 2.1 31.3 1.0
CG B:ASP177 2.9 44.9 1.0
CE1 B:HIS203 2.9 27.1 1.0
CE1 B:HIS190 2.9 31.1 1.0
CE1 B:HIS175 2.9 38.4 1.0
CD2 B:HIS175 3.0 42.2 1.0
CG B:HIS203 3.1 23.8 1.0
CD2 B:HIS190 3.1 26.0 1.0
OD2 B:ASP177 3.2 44.0 1.0
CB B:HIS203 3.5 23.3 1.0
ND1 B:HIS175 4.0 38.7 1.0
NE2 B:HIS203 4.0 29.0 1.0
O B:TYR179 4.0 43.6 1.0
ND1 B:HIS190 4.1 33.6 1.0
CG B:HIS175 4.1 41.4 1.0
CB B:ASP177 4.2 44.4 1.0
CD2 B:HIS203 4.2 24.7 1.0
CG B:HIS190 4.2 28.4 1.0
CE2 B:PHE192 4.3 30.1 1.0
CZ B:PHE192 4.4 32.0 1.0
CZ B:PHE181 4.6 30.7 1.0
CE2 B:PHE181 4.7 37.7 1.0
CB B:TYR179 4.9 45.0 1.0
CA B:HIS203 5.0 23.8 1.0

Reference:

C.Antoni, L.Vera, L.Devel, M.P.Catalani, B.Czarny, E.Cassar-Lajeunesse, E.Nuti, A.Rossello, V.Dive, E.A.Stura. Crystallization of Bi-Functional Ligand Protein Complexes. J.Struct.Biol. V. 182 246 2013.
ISSN: ISSN 1047-8477
PubMed: 23567804
DOI: 10.1016/J.JSB.2013.03.015
Page generated: Sun Oct 27 00:11:22 2024

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